Federal regulators have cited the city of Seattle for illegally filling wetlands and a portion of Hamm Creek in Southwest Seattle during a major construction project.

Responding to a complaint lodged on Earth Day, the U.S. Army Corps of Engineers notified the city May 12 that its $26 million Joint Training Facility project had filled a half acre of wetlands without obtaining a Corps permit — a violation of federal law, according to a letter signed by Col. Debra Lewis, head of the agency’s Seattle district.

City officials said they are cooperating with the Corps and may suggest wetlands restoration at other sites to make up for the error.

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“We are very concerned about the environmental issues, and we will appropriately address them,” said Brenda Bauer, director of the city’s Fleets and Facilities Department. However, she also said the city was researching whether the Corps had jurisdiction over the site and whether wetlands and a creek really exist there at all.

Though some minor paving and grading work has been halted by the Corps’ order, construction on the main buildings continues, Bauer said. “This isn’t stopping the project,” which is nearly 70 percent complete, she added.

Located on a 13-acre parcel that was once a gravel quarry, the Joint Training Facility was funded largely by a voter-approved $167 million fire-station and emergency-preparedness levy two years ago. It includes classrooms and buildings for staging mock fires and other disasters to train firefighters and utility workers.

The wetlands problem came to the Corps’ attention when Lewis was approached at an Earth Day tree-planting ceremony by John Beal, a South Seattle activist who has worked for decades to restore Hamm Creek, a previously blighted urban stream that feeds into the Duwamish River.

Beal said he told Lewis the city had filled in wetlands and otherwise encroached on his beloved creek while ignoring his complaints. He also claimed sediment from the construction site has been flowing downstream and clogging up other parts of the stream.

“I’m not against this project. I’m against the way they’ve done it,” Beal said. “They’ve not taken any of the ecology or the stream into consideration. What they’ve done is unacceptable.”

A subsequent visit by a Corps inspector found merit to at least some of Beal’s claims.

The Corps action was somewhat of an embarrassment for Seattle officials, who usually take pride in their environmentalist credentials.

The Joint Training Center, for example, was designed to meet a rigorous “Green Building” standard set by a national builder group. “It is rare for the city, a strong environmental steward, to find itself in other than a leadership role on environmental issues,” Bauer said in a written response to Lewis.

The violations cited by the Corps could carry fines of up to $25,000 a day, but Corps officials said they are not inclined to impose monetary penalties if the city agrees to perform restoration work on other nearby wetlands.

“We still want to know why they went ahead and did this work without a permit,” said John Pell, project manager for the agency’s enforcement section, who inspected the site. “Everyone knows they should have done it.”

Bauer said she was still investigating why the city did not obtain a permit.

The construction project has been headed by Shiels Obletz Johnsen, a project-management firm, since last October, when the city removed its own manager from the job for what Bauer described as “cost concerns.”

A call to Shiels Obletz Johnsen was not returned yesterday.

Bauer questioned whether Hamm Creek really flows through the site, though the city’s Web site contains a drawing of the construction site with the creek clearly marked. She also said she was not sure whether the water that flows from the site could have caused sediment buildup downstream, as Beal has claimed.

“I’d challenge you to find some straight path between our site and the creek down below,” Bauer said.

Beal said there is no question that a couple of forks of the creek flow through the site. He said he’d been assured by city officials, including Mayor Greg Nickels, that the project would be conducted in a way that didn’t harm the wetlands or the creek, which has become a prized urban habitat for salmon and trout downstream.

Beal said he expected better of a city that often preaches environmentalism to the rest of the country.